scholarly journals Scaling laws in enzyme function reveal a new kind of biochemical universality

2021 ◽  
Author(s):  
Dylan C. Gagler ◽  
Bradley Karas ◽  
Chris Kempes ◽  
Aaron D. Goldman ◽  
Hyunju Kim ◽  
...  
Keyword(s):  
Scaling Laws ◽  
Chemical Compounds ◽  
Last Universal Common Ancestor ◽  
Detailed Model ◽  
Shared Set ◽  
Universal Common Ancestor ◽  
Universality Classes ◽  
Synthetic Life ◽  
Life On Earth ◽  
Enzyme Functions

AbstractAll life on Earth is unified by its use of a shared set of component chemical compounds and reactions, providing a detailed model for universal biochemistry. However, this notion of universality is specific to currently observed biochemistry and does not allow quantitative predictions about examples not yet observed. Here we introduce a more generalizable concept of biochemical universality, more akin to the kind of universality discussed in physics. Using annotated genomic datasets including an ensemble of 11955 metagenomes and 1282 archaea, 11759 bacteria and 200 eukaryotic taxa, we show how four of the major enzyme functions - the oxidoreductases, transferases, hydrolases and ligases - form universality classes with common scaling behavior in their relative abundances observed across the datasets. We verify these universal scaling laws are not explained by the presence of compounds, reactions and enzyme functions shared across all known examples of life. We also demonstrate how a consensus model for the last universal common ancestor (LUCA) is consistent with predictions from these scaling laws, with the exception of ligases and transferases. Our results establish the existence of a new kind of biochemical universality, independent of the details of the component chemistry, with implications for guiding our search for missing biochemical diversity on Earth, or other for any biochemistries that might deviate from the exact chemical make-up of life as we know it, such as at the origins of life, in alien environments, or in the design of synthetic life.

scholarly journals The structural proteome for the primordial glycolysis/gluconeogenesis

2019 ◽  
Author(s):  
Isabela Jerônimo Bezerra do Ó ◽  
Thais Gaudêncio Rego ◽  
Marco V. José ◽  
Sávio Torres de Farias
Keyword(s):  
Common Ancestor ◽  
Simple Function ◽  
Last Universal Common Ancestor ◽  
Origin And Evolution ◽  
Ancestral Sequences ◽  
Catalytic Function ◽  
Universal Common Ancestor ◽  
Evolution Of Life ◽  
Catalytic Sites ◽  
Life On Earth

AbstractComprehending the constitution of early biological metabolism is indispensable for the understanding of the origin and evolution of life on Earth. Here, we analyzed the structural proteome before the Last Universal Common Ancestor (LUCA) based in the reconstruction of the ancestral sequences and structure for proteins involved in glycolysis/gluconeogenesis. The results are compatible with the notion that the first portions of the proteins were the areas homologous to the present-day catalytic sites. Those “proto-proteins” had a simple function: binding to cofactors. Upon the accretion of new elements to the structure, the catalytic function could have emerged. Also, the first structural motifs might have been related to the emergence of the different proteins that work in modern organisms.

scholarly journals Universal and taxon-specific trends in protein sequences as a function of age

2020 ◽  
Author(s):  
Jennifer E James ◽  
Sara M Willis ◽  
Paul G Nelson ◽  
Catherine Weibel ◽  
Luke J Kosinski ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Young Animal ◽  
Structural Disorder ◽  
Last Universal Common Ancestor ◽  
Protein Coding ◽  
Universal Common Ancestor ◽  
Eukaryotic Species ◽  
Life On Earth ◽  
Hydrophobic Clustering

AbstractExtant protein-coding sequences span a huge range of ages, from those that emerged only recently in particular lineages, to those present in the last universal common ancestor. Because evolution has had less time to act on young sequences, there might be “phylostratigraphy” trends in any properties that evolve slowly with age. Indeed, a long-term reduction in hydrophobicity and in hydrophobic clustering has been found in previous, taxonomically restricted studies. Here we perform integrated phylostratigraphy across 435 fully sequenced and dated eukaryotic species, using sensitive HMM methods to detect homology of protein domains (which may vary in age within the same gene), and applying a variety of quality filters. We find that the reduction in hydrophobic clustering is universal across diverse lineages, showing limited sign of saturation. But the tendency for young domains to have higher protein structural disorder, driven primarily by more hydrophilic amino acids, is found only among young animal domains, and not young plant domains, nor ancient domains predating the existence of the last eukaryotic common ancestor. Among ancient domains, trends in amino acid composition reflect the order of recruitment into the genetic code, suggesting that events during the earliest stages of life on earth continue to have an impact on the composition of ancient sequences.

scholarly journals Reconstructing gene content in the last common ancestor of cellular life: is it possible, should it be done, and are we making any progress?

2014 ◽  
Author(s):  
Arcady Mushegian
Keyword(s):  
Evolutionary Biology ◽  
Common Ancestor ◽  
Recent Literature ◽  
Last Common Ancestor ◽  
Gene Repertoire ◽  
Ancestral State ◽  
Last Universal Common Ancestor ◽  
Cellular Life ◽  
Universal Common Ancestor ◽  
Life On Earth

I review recent literature on the reconstruction of gene repertoire of the Last Universal Common Ancestor of cellular life (LUCA). The form of the phylogenetic record of cellular life on Earth is important to know in order to reconstruct any ancestral state; therefore I also discuss the emerging understanding that this record does not take the form of a tree. I argue that despite this, “tree-thinking” remains an essential component in evolutionary thinking and that “pattern pluralism” in evolutionary biology can be only epistemological, but not ontological.

scholarly journals The Prebiotic Stage and the Evolution of Life on Earth

2019 ◽  
Vol 9 (2) ◽  
pp. 86
Author(s):  
Gogu Ghiorghita ◽  
Gheorghe Surpateanu
Keyword(s):  
Molecular Nitrogen ◽  
Big Bang ◽  
Free Atmosphere ◽  
Last Universal Common Ancestor ◽  
Origin And Evolution ◽  
Cellular Energy ◽  
Universal Common Ancestor ◽  
Evolution Of Life ◽  
Life On Earth ◽  
Multicellular Organisms

The paper is a synthesis of the information collected so far on the origin and evolution of life on Earth. The life appearance and its evolution is correlated to matter evolution in univers: Big Bang, inorganic, organic, prebiotic, unicellular and multicellular stages. Concerning prebiotic stage in life evolution we present our theory based on syntone chemistry. Three syntones-methylene, nitrene and carbon monoxid carried by molecular nitrogen at law temperature could furnish the prebiotic bricks (sugars, lipids, proteins) at the contact to primary atmosphere components. Also, we think that these syntones could be considered as sources of great number of organic molecules. All organisms on Earth descend from a last universal common ancestor (LUCA). Two branches were derived from LUCA: one led to bacteria and the other to archaea and eukaryotes. The appearance of photosynthesis determined a transition from the oxygen-free atmosphere to the oxic atmosphere. Due to a series of endosymbioses, Eukaryotes emerged as organisms with nucleated cells and aerobic metabolism (which significantly increased the efficiency of cellular energy production). At about the same time appeared the first multicellular organisms. The paper also presents other important moments in the evolution of life on Earth, including the major biological crises in certain periods, resulting in the mass extinction of some groups of organisms. The evolution of the living world on Earth culminated with the emergence of man, the most complex being with language, superior thinking, emotions, creativity, etc.

scholarly journals SepF is the FtsZ anchor in archaea, with features of an ancestral cell division system

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Nika Pende ◽  
Adrià Sogues ◽  
Daniela Megrian ◽  
Anna Sartori-Rupp ◽  
Patrick England ◽  
...  
Keyword(s):  
Cell Division ◽  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
Super Resolution ◽  
Binding Mode ◽  
Last Universal Common Ancestor ◽  
Division Plane ◽  
Multiple Factors ◽  
Universal Common Ancestor ◽  
Super Resolution Microscopy

AbstractMost archaea divide by binary fission using an FtsZ-based system similar to that of bacteria, but they lack many of the divisome components described in model bacterial organisms. Notably, among the multiple factors that tether FtsZ to the membrane during bacterial cell constriction, archaea only possess SepF-like homologs. Here, we combine structural, cellular, and evolutionary analyses to demonstrate that SepF is the FtsZ anchor in the human-associated archaeon Methanobrevibacter smithii. 3D super-resolution microscopy and quantitative analysis of immunolabeled cells show that SepF transiently co-localizes with FtsZ at the septum and possibly primes the future division plane. M. smithii SepF binds to membranes and to FtsZ, inducing filament bundling. High-resolution crystal structures of archaeal SepF alone and in complex with the FtsZ C-terminal domain (FtsZCTD) reveal that SepF forms a dimer with a homodimerization interface driving a binding mode that is different from that previously reported in bacteria. Phylogenetic analyses of SepF and FtsZ from bacteria and archaea indicate that the two proteins may date back to the Last Universal Common Ancestor (LUCA), and we speculate that the archaeal mode of SepF/FtsZ interaction might reflect an ancestral feature. Our results provide insights into the mechanisms of archaeal cell division and pave the way for a better understanding of the processes underlying the divide between the two prokaryotic domains.

scholarly journals Origin of Life

2021 ◽  
Vol 83 (2) ◽  
pp. 76-79
Author(s):  
Cristina Sousa
Keyword(s):  
Origin Of Life ◽  
Common Ancestor ◽  
Scientific Evidence ◽  
Recent Common Ancestor ◽  
Last Universal Common Ancestor ◽  
Most Recent Common Ancestor ◽  
Universal Common Ancestor ◽  
The Origin Of Life

The origin of life is one of the most interesting and challenging questions in biology. This article discusses relevant contemporary theories and hypotheses about the origin of life, recent scientific evidence supporting them, and the main contributions of several scientists of different nationalities and specialties in different disciplines. Also discussed are several ideas about the characteristics of the most recent common ancestor, also called the “last universal common ancestor” (or LUCA), including cellular status (unicellular or community) and homogeneity level.

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